NM_032664.3:c.376+13765A>C

Variant names:

• chr8-33439451-T-G
• rs938641
• NM_032664.3:c.376+13765A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032664.3(POFUT3):​c.376+13765A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,006 control chromosomes in the GnomAD database, including 34,608 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34608 hom., cov: 32)
• Consequence: POFUT3 NM_032664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 7 publications found

Genes affected

POFUT3 (HGNC:19234): (fucosyltransferase 10) Predicted to enable alpha-(1->3)-fucosyltransferase activity. Predicted to be involved in fucosylation. Predicted to act upstream of or within cerebral cortex radially oriented cell migration and neuronal stem cell population maintenance. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POFUT3	NM_032664.3	c.376+13765A>C		intron_variant	Intron 3 of 4	ENST00000327671.10	NP_116053.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT10	ENST00000327671.10	c.376+13765A>C		intron_variant	Intron 3 of 4	1	NM_032664.3	ENSP00000332757.5

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101639 AN: 151888 Hom.: 34589 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.644

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.669 AC: 101707 AN: 152006 Hom.: 34608 Cov.: 32 AF XY: 0.666 AC XY: 49508 AN XY: 74298

African (AFR) AF: 0.781 AC: 32378 AN: 41456

American (AMR) AF: 0.567 AC: 8656 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3011 AN: 5150

South Asian (SAS) AF: 0.509 AC: 2459 AN: 4828

European-Finnish (FIN) AF: 0.653 AC: 6900 AN: 10562

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44041 AN: 67966

Other (OTH) AF: 0.644 AC: 1357 AN: 2106

Alfa AF: 0.591 Hom.: 3057

Bravo AF: 0.668

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.65
DANN	Benign	0.36
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs938641; hg19: chr8-33296969;